Update...
I just got back from Industrial Injection in SLC and we are stumped! Here's what happened in chronological order.
First, the tech hooked up the DRB3 to clear all the codes I generated when unplugging sensors while the engine was running. These codes did not come back, nor did any new ones.
Next, he ran the injector kill test and the rpms dropped like they should equally as each injector was shut off. He repeated the kill test again for verification.
Then we monitored the rail pressure and it was pretty much dead on 5300 psi setpoint and actual. Playing with the throttle from idle rpm up showed that the actual rail pressure followed the rail pressure setpoint fairly closely with no big variances suggesting that the CP3 / FCA / rail pressure relief valve were good.
Next we went for a 30 minute drive and I duplicated the issue numerous times. He monitored all sensors, including cam and crank (crank especially for injection timing) as well as the rail pressure and any codes and everything checked fine! Actual rail pressure was close to setpoint the whole time with no wild variances suggesting that the FCA was the culprit, the crank and cam sensors had the appropriate "square curve" happening on the graph, and no codes - nada injection misfire - nothing! Again, this strongly suggested all sensors were good as well as the CP3. Weird juju going on with no "smoking gun".
So we pulled back into the shop and discussed what could be happening. He said that he had looked at about 30 - 3rd gens with a similar sort of problem as mine and 10 of them had to have their ECMs reflashed or replaced due to all the chips/boxes they have been running (note I had run the BDDL programmer before). So before he could diagnose further he wanted the ECM eliminated from the picture. A quick phone call to Hinckley Dodge and I was getting my ECM reflashed 15 minutes later. The dealer tech commented that my idle felt rough seat-of-pants and I responded that was something we were trying to diagnose yet the dash tach or DRB tach doesn't show an idle variation.
After the reflash and with fingers crossed I leave the dealership and feather the throttle from idle to ~1700 rpms and... "poof-sputter-poof-clickity clack" and then takes off fine! Crap...
So I went back to Industrial Injection and talked to the tech again and he came up with some possibilities:
1) sticking injector that's not firing or is firing, but may be carboned up.
2) cracked nozzle (one of the heavily modded 3rd gens mentioned above had this problem as well as the bad ECM)
3) poor wiring connection somewhere
4) Air in fuel (can lead to retarded injection according to my Tech Authority Cummins HPCR class book)
5) broken valve springs that's not letting the compression build
6) dropped valve seat or loose valve seat (history of this on 2003's according to tech)
We agreed that 5) and 6) might be farfetched since the issue is only happening at a certain rpm. That is, if it was a mechanical issue, then my engine would be making noise all the time and/or oil pressure would go bad and/or fuel in oil and/or siezed engine???
Anyhow, I got an appointment set up for next Thursday and they will pull all my injectors and go through them. When my truck cools down, I will pull the valve cover and check my injector electrical connections and check for unusual valve movement or broken springs. I will also check the CP3 fuel feed line for any air leaks.
I'm also going to take my infrared heat gun and measure the exhaust runner temps for each cylinder and see if there's any difference.
I also have a spare crank sensor (as well as spare pressure relief valve, map sensor,

) that I will try just in case. The tech did say that sometimes the sensor can develop "flat spots" that do not generate codes, but can cause certain driveability issues.
Maybe in the end it could be the CP3, who knows! I just do not want to spend that kind of money yet until I go through the other things first.
Other than the above it was a fairly uneventful day!